Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut

Grégory Dubourg; Aurélie Morand; Fatima Mekhalif; Raphael Godefroy; Alice Corthier; Abdourahamane Yacouba; Ami Diakite; Florent Cornu; Marina Cresci; Samy Brahimi; Aurélia Caputo; Eric Lechevallier; Michel Tsimaratos; Valérie Moal; Jean-Christophe Lagier; Didier Raoult

doi:10.3389/fmicb.2020.513305

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut

Front Microbiol. 2020 Oct 16:11:513305. doi: 10.3389/fmicb.2020.513305. eCollection 2020.

Authors

Grégory Dubourg¹, Aurélie Morand^{1

2}, Fatima Mekhalif^{1

3}, Raphael Godefroy^{1

3}, Alice Corthier^{1

3}, Abdourahamane Yacouba^{1

3}, Ami Diakite^{1

3}, Florent Cornu¹, Marina Cresci¹, Samy Brahimi^{1

3}, Aurélia Caputo¹, Eric Lechevallier⁴, Michel Tsimaratos⁵, Valérie Moal^{1

6}, Jean-Christophe Lagier¹, Didier Raoult¹

Affiliations

¹ IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France.
² Pédiatrie Spécialisée et Médecine Infantile, Hôpital de la Timone, AP-HM, Marseille, France.
³ Fondation Méditerranée Infection, Marseille, France.
⁴ Department of Urology and Renal Transplantation, La Conception University Hospital, AP-HM, Aix-Marseille University, Marseille, France.
⁵ Pédiatrie Multidisciplinaire, Hôpital de la Timone, AP-HM, Marseille, France.
⁶ Centre de Nephrologie et Transplantation Rénale, Hôpital de la Conception, Aix-Marseille University, Marseille, France.

Abstract

Human urine was considered sterile for a long time. However, 416 species have been previously cultured, including only 40 anaerobic species. Here, we used culturomics, particularly those targeting anaerobes, to better understand the urinary microbiota. By testing 435 urine samples, we isolated 450 different bacterial species, including 256 never described in urine of which 18 were new species. Among the bacterial species identified, 161 were anaerobes (35%). This study increased the known urine repertoire by 39%. Among the 672 bacterial species isolated now at least once from urine microbiota, 431 (64.1%) were previously isolated from gut microbiota, while only 213 (31.7%) were previously isolated from vagina. These results suggest that many members of the microbiota in the urinary tract are in fact derived from the gut, and a paradigm shift is thus needed in our understanding.

Keywords: bladder; culture; culturomics; microbiota; urine.